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Persistent homology

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https://www.readbyqxmd.com/read/28714850/high-resolution-mapping-of-heteroduplex-dna-formed-during-uv-induced-and-spontaneous-mitotic-recombination-events-in-yeast
#1
Yi Yin, Margaret Dominska, Eunice Yim, Thomas D Petes
In yeast, DNA breaks are usually repaired by homologous recombination (HR). An early step for HR pathways is formation of a heteroduplex, in which a single-strand from the broken DNA molecule pairs with a strand derived from an intact DNA molecule. If the two strands of DNA are not identical, there will be mismatches within the heteroduplex DNA (hetDNA). In wild-type strains, these mismatches are repaired by the mismatch repair (MMR) system, producing a gene conversion event. In strains lacking MMR, the mismatches persist...
July 17, 2017: ELife
https://www.readbyqxmd.com/read/28713014/a-recombinant-type-2-porcine-reproductive-and-respiratory-syndrome-virus-between-nadc30-like-and-a-mlv-like-genetic-characterization-and-pathogenicity-for-piglets
#2
Ting Bian, Yingfeng Sun, Meng Hao, Lei Zhou, Xinna Ge, Xin Guo, Jun Han, Hanchun Yang
Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically important pathogen for swine industry worldwide. The recombination occurring among PRRSV strains has been recognized as one of important molecular mechanisms for the evolution of PRRSV. Current prevalence of PRRSV NADC30-like causing clinical disease outbreaks is highly concerned in China. In the present study, the genetic characterization of a recombinant type 2 PRRSV (designated TJnh1501) was analyzed and its pathogenicity for piglets was examined...
July 13, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28708585/the-neglected-avian-hepatotropic-virus-induces-acute-and-chronic-hepatitis-in-ducks-an-alternative-model-for-hepatology
#3
Xumin Ou, Sai Mao, Jingyu Cao, Yunchao Ma, Guangpeng Ma, Anchun Cheng, Mingshu Wang, Dekang Zhu, Shun Chen, Renyong Jia, Mafeng Liu, Kunfeng Sun, Qiao Yang, Ying Wu, Xiaoyue Chen
Duck Hepatitis A Virus (DHAV) belongs to the Avihepatovirus, which is also classified into Picornaviridae with Hepatovirus, Hepatitis A Virus (HAV). In humans, the pathogenesis of HAV is not well understood because of limited work with animal models. Here, we investigated the progress of duck viral hepatitis caused by DHAV and their potential for dissecting the pathogenesis of HAV. During the course of infection, the duck model had undergone hepatocellular lesions (vacuolation, acidophilic degeneration and steatosis), lymphocytes recruitment (neutrophil granulocytes, heterophilic granulocytes and T cells or plasm cells) and repair (activation of hepatic stellate cells, fibrosis and regeneration)...
July 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28704921/eys-mutations-causing-autosomal-recessive-retinitis-pigmentosa-changes-of-retinal-structure-and-function-with-disease-progression
#4
David B McGuigan, Elise Heon, Artur V Cideciyan, Rinki Ratnapriya, Monica Lu, Alexander Sumaroka, Alejandro J Roman, Vaishnavi Batmanabane, Alexandra V Garafalo, Edwin M Stone, Anand Swaroop, Samuel G Jacobson
Mutations in the EYS (eyes shut homolog) gene are a common cause of autosomal recessive (ar) retinitis pigmentosa (RP). Without a mammalian model of human EYS disease, there is limited understanding of details of disease expression and rates of progression of the retinal degeneration. We studied clinically and with chromatic static perimetry, spectral-domain optical coherence tomography (OCT), and en face autofluoresence imaging, a cohort of 15 patients (ages 12-51 at first visit), some of whom had longitudinal data of function and structure...
July 12, 2017: Genes
https://www.readbyqxmd.com/read/28694793/comparative-genomic-characterization-of-the-highly-persistent-and-potentially-virulent-cronobacter-sakazakii-st83-cc65-strain-h322-and-other-st83-strains
#5
Hannah R Chase, Gopal R Gopinath, Athmanya K Eshwar, Andrea Stoller, Claudia Fricker-Feer, Jayanthi Gangiredla, Isha R Patel, Hediye N Cinar, HyeJin Jeong, ChaeYoon Lee, Flavia Negrete, Samantha Finkelstein, Roger Stephan, Ben D Tall, Angelika Lehner
Cronobacter (C.) sakazakii is an opportunistic pathogen and has been associated with serious infections with high mortality rates predominantly in pre-term, low-birth weight and/or immune compromised neonates and infants. Infections have been epidemiologically linked to consumption of intrinsically and extrinsically contaminated lots of reconstituted powdered infant formula (PIF), thus contamination of such products is a challenging task for the PIF producing industry. We present the draft genome of C. sakazakii H322, a highly persistent sequence type (ST) 83, clonal complex (CC) 65, serotype O:7 strain obtained from a batch of non-released contaminated PIF product...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28694656/helicobacter-pylori-baba-in-adaptation-for-gastric-colonization
#6
REVIEW
Shamshul Ansari, Yoshio Yamaoka
Helicobacter pylori (H. pylori) as a causative agent of gastric complications, is well adapted for the colonization of gastric mucosa. Although the infectious process depends on several factors, the adhesion to the gastric mucosa is the first and important step. Among several outer membrane proteins, BabA is one of the significant protein involving in many inflammatory processes in addition to its role in the attachment for the persistent colonization. We performed a PubMed search using the key words: "babA", "pylori", "gastric complications", "homologous recombination", "slipped strand mispairing"; a total of 249 articles were displayed...
June 21, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28694245/fundamental-cell-cycle-kinases-collaborate-to-ensure-timely-destruction-of-the-synaptonemal-complex-during-meiosis
#7
Bilge Argunhan, Wing-Kit Leung, Negar Afshar, Yaroslav Terentyev, Vijayalakshmi V Subramanian, Yasuto Murayama, Andreas Hochwagen, Hiroshi Iwasaki, Tomomi Tsubouchi, Hideo Tsubouchi
The synaptonemal complex (SC) is a proteinaceous macromolecular assembly that forms during meiotic prophase I and mediates adhesion of paired homologous chromosomes along their entire lengths. Although prompt disassembly of the SC during exit from prophase I is a landmark event of meiosis, the underlying mechanism regulating SC destruction has remained elusive. Here, we show that DDK (Dbf4-dependent Cdc7 kinase) is central to SC destruction. Upon exit from prophase I, Dbf4, the regulatory subunit of DDK, directly associates with and is phosphorylated by the Polo-like kinase Cdc5...
July 10, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28691128/virulent-strain-of-african-swine-fever-virus-eclipses-its-attenuated-derivative-after-challenge
#8
Ilya Titov, Galina Burmakina, Yuriy Morgunov, Sergey Morgunov, Andrey Koltsov, Alexander Malogolovkin, Denis Kolbasov
African swine fever (ASF) is one of the most devastating diseases affecting the swine industry worldwide. No effective vaccine is currently available for disease prevention and control. Although live attenuated vaccines (LAV) have demonstrated great potential for immunizing against homologous strains of African swine fever virus (ASFV), adverse reactions from LAV remain a concern. Here, by using a homologous ASFV Congo strain system, we show passage-attenuated Congo LAV to induce an efficient protective immune response against challenge with the virulent parental Congo strain...
July 10, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28689921/the-novel-mef-c-mph-g-macrolide-resistance-genes-are-conveyed-in-the-environment-on-various-vectors
#9
Yuta Sugimoto, Satoru Suzuki, Lisa Nonaka, Chanchai Boonla, Nop Sukpanyatham, Hsin-Yiu Chou, Jer-Horng Wu
BACKGROUND: The novel tandem genes mef(C) and mph(G) have been reported in marine bacteria in Japan. This paper aimed to characterise the extent of environmental distribution of mef(C) and mph(G) as well as their dissemination and persistence in aquatic bacterial communities. METHODS: Erythromycin-resistant bacteria were isolated from Japan, Taiwan and Thailand aquaculture sites. The mef(C)-mph(G) genes were detected by PCR. The size of mobile genetic elements conveying mef(C) and mph(G) was examined by Southern blotting...
July 6, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28687608/thioredoxin-reductase-from-toxoplasma-gondii-an-essential-virulence-effector-with-antioxidant-function
#10
Junxin Xue, Wei Jiang, Yongjun Chen, Fengju Gong, Minyan Wang, Peng Zeng, Can Xia, Quan Wang, Kehe Huang
Thioredoxin reductase (TR) can help pathogens resist oxidative-burst injury from host immune cells by maintaining a thioredoxin-reduction state during NADPH consumption. TR is a necessary virulence factor that enables the persistent infection of some parasites. We performed bioinformatics analyses and biochemical assays to characterize the activity, subcellular localization, and genetic ablation of Toxoplasma gondii TR (TgTR), to shed light on its biologic function. We expressed the TgTR protein with an Escherichia coli expression system and analyzed its enzyme activity, reporting a Km for the recombinant TgTR of 11...
July 7, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28677268/integration-of-element-specific-persistent-homology-and-machine-learning-for-protein-ligand-binding-affinity-prediction
#11
Zixuan Cang, Guo Wei Wei
Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, gene expression, etc. Accurate prediction of protein-ligand binding affinities is vital to rational drug design and the understanding of protein-ligand binding and binding induced function. Existing binding affinity prediction methods are inundated with geometric detail and involve excessively high dimensions, which undermines their predictive power for massive binding data...
July 5, 2017: International Journal for Numerical Methods in Biomedical Engineering
https://www.readbyqxmd.com/read/28674176/effects-of-chronic-social-defeat-stress-on-sleep-and-circadian-rhythms-are-mitigated-by-kappa-opioid-receptor-antagonism
#12
Audrey M Wells, Elysia Ridener, Clinton A Bourbonais, Woori Kim, Harry Pantazopoulos, F Ivy Carroll, Kwang-Soo Kim, Bruce M Cohen, William A Carlezon
Stress plays a critical role in the neurobiology of mood and anxiety disorders. Sleep and circadian rhythms are affected in many of these conditions. Here we examined the effects of chronic social defeat stress (CSDS), an ethological form of stress, on sleep and circadian rhythms. We exposed male mice implanted with wireless telemetry transmitters to a 10-day CSDS regimen known to produce anhedonia (a depressive-like effect) and social avoidance (an anxiety-like effect). Electroencephalography (EEG), electromyography (EMG), body temperature, and locomotor activity data were collected continuously during the CSDS regimen and a 5-day recovery period...
July 3, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28674066/contribution-of-the-chromosomal-ccdab-operon-to-bacterial-drug-tolerance
#13
Kritika Gupta, Arti Tripathi, Alishan Sahu, Raghavan Varadarajan
One of the first identified and best studied toxin-antitoxin systems in Escherichia coli is the F-plasmid based CcdAB system. This system is involved in plasmid maintenance through post-segregational killing. More recently, ccdAB homologs have been found on the chromosome, including in pathogenic strains of E. coli and other bacteria. However the functional role of chromosomal ccdAB genes, if any, has remained unclear. We show that both the native ccd operon of the E.coliO157 strain, as well as the ccd operon from the F- plasmid, when inserted on the E...
July 3, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28666126/telomere-length-determines-terra-and-r-loop-regulation-through-the-cell-cycle
#14
Marco Graf, Diego Bonetti, Arianna Lockhart, Kamar Serhal, Vanessa Kellner, André Maicher, Pascale Jolivet, Maria Teresa Teixeira, Brian Luke
Maintenance of a minimal telomere length is essential to prevent cellular senescence. When critically short telomeres arise in the absence of telomerase, they can be repaired by homology-directed repair (HDR) to prevent premature senescence onset. It is unclear why specifically the shortest telomeres are targeted for HDR. We demonstrate that the non-coding RNA TERRA accumulates as HDR-promoting RNA-DNA hybrids (R-loops) preferentially at very short telomeres. The increased level of TERRA and R-loops, exclusively at short telomeres, is due to a local defect in RNA degradation by the Rat1 and RNase H2 nucleases, respectively...
June 29, 2017: Cell
https://www.readbyqxmd.com/read/28663751/lactoferrin-efficiently-counteracts-the-inflammation-induced-changes-of-the-iron-homeostasis-system-in-macrophages
#15
Antimo Cutone, Luigi Rosa, Maria Stefania Lepanto, Mellani Jinnett Scotti, Francesca Berlutti, Maria Carmela Bonaccorsi di Patti, Giovanni Musci, Piera Valenti
Human lactoferrin (hLf), an 80-kDa multifunctional iron-binding cationic glycoprotein, is constitutively secreted by exocrine glands and by neutrophils during inflammation. hLf is recognized as a key element in the host immune defense system. The in vitro and in vivo experiments are carried out with bovine Lf (bLf), which shares high sequence homology and identical functions with hLf, including anti-inflammatory activity. Here, in "pure" M1 human macrophages, obtained by stimulation with a mixture of 10 pg/ml LPS and 20 ng/ml IFN-γ, as well as in a more heterogeneous macrophage population, challenged with high-dose of LPS (1 µg/ml), the effect of bLf on the expression of the main proteins involved in iron and inflammatory homeostasis, namely ferroportin (Fpn), membrane-bound ceruloplasmin (Cp), cytosolic ferritin (Ftn), transferrin receptor 1, and cytokines has been investigated...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28658280/reversible-perturbations-of-gene-regulation-after-genome-editing-in-drosophila-cells
#16
Stefan Kunzelmann, Klaus Förstemann
The prokaryotic phage defense CRISPR/cas-system has developed into a versatile toolbox for genome engineering and genetic studies in many organisms. While many efforts were spent on analyzing the consequences of off-target effects, only few studies addressed side-effects that occur due to the targeted manipulation of the genome. Here, we show that the CRISPR/cas9-mediated integration of an epitope tag in combination with a selection cassette can trigger an siRNA-mediated, epigenetic genome surveillance pathway in Drosophila melanogaster cells...
2017: PloS One
https://www.readbyqxmd.com/read/28643456/irf6-expression-in-basal-epithelium-partially-rescues-irf6-knockout-mice
#17
Youssef A Kousa, Dina Moussa, Brian C Schutte
BACKGROUND: Mutations in IRF6, CHUK (IKKA) and RIPK4 can lead to a disease spectrum that includes cutaneous, limb and craniofacial malformations. Loss of these alleles in the mouse leads to perinatal lethality and severe cutaneous, limb and craniofacial defects. Genetic rescue in the mouse has been shown for Ikka and Ripk4. RESULTS: Here, we show partial genetic rescue of Irf6 knockout embryos using the KRT14 promoter to drive Irf6 expression in the basal epithelium...
June 23, 2017: Developmental Dynamics: An Official Publication of the American Association of Anatomists
https://www.readbyqxmd.com/read/28642841/strain-and-dose-dependent-reduction-of-toxoplasma-gondii-burden-in-pigs-is-associated-with-interferon-gamma-production-by-cd8-lymphocytes-in-a-heterologous-challenge-model
#18
Malgorzata Jennes, Stéphane De Craeye, Bert Devriendt, Katelijne Dierick, Pierre Dorny, Eric Cox
Toxoplasma gondii is a worldwide prevalent parasite of humans and animals. The global infection burden exceeds yearly one million disability-adjusted life years (DALY's) in infected individuals. Therefore, effective preventive measures should be taken to decrease the risk of infection in humans. Although human toxoplasmosis is predominantly foodborne by ingestion of tissue cysts in meat from domestic animals such as pigs, the incidence risk is difficult to estimate due to the lack of screening of animals for infection and insights in location and persistence of the parasite in the tissues...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28635037/novel-role-and-regulation-of-hdac4-in-cocaine-related-behaviors
#19
Rachel D Penrod, Maria B Carreira, Makoto Taniguchi, Jaswinder Kumar, Stephanie A Maddox, Christopher W Cowan
Epigenetic mechanisms have been proposed to contribute to persistent aspects of addiction-related behaviors. One family of epigenetic molecules that may regulate maladaptive behavioral changes produced by cocaine use are the histone deacetylases (HDACs)-key regulators of chromatin and gene expression. In particular, the class IIa HDACs (HDAC4, HDAC5, HDAC7 and HDAC9) respond to changes in neuronal activity by modulating their distribution between the nucleus and cytoplasm-a process controlled in large part by changes in phosphorylation of conserved residues...
June 21, 2017: Addiction Biology
https://www.readbyqxmd.com/read/28632940/characterization-of-the-i4399m-variant-of-apolipoprotein-a-implications-for-altered-prothrombotic-properties-of-lipoprotein-a
#20
Corey A Scipione, Jackson T McAiney, Daniel J Simard, Zainab A Bazzi, Matthew Gemin, Rocco Romagnuolo, Fraser L Macrae, Robert A Ariëns, Robert A Hegele, Janeen Auld, James W Gauld, Michael B Boffa, Marlys L Koschinsky
BACKGROUND: Lipoprotein(a) (Lp(a)) is a causal risk factor for a variety of cardiovascular diseases. Apolipoprotein(a) (apo(a)), the distinguishing component of Lp(a), is homologous to plasminogen, suggesting that Lp(a) can interfere with the normal fibrinolytic functions of plasminogen. This has implications for the persistence of fibrin clots in the vasculature and hence to atherothrombotic diseases. A single nucleotide polymorphism (rs3798220) in the gene encoding apo(a) has been reported that results in an Ile to Met substitution in the protease-like domain (I4399M variant)...
June 20, 2017: Journal of Thrombosis and Haemostasis: JTH
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